GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-5

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p>orresponds to a result sub-graph. Each column's header contains two lines: the first one indicates the label of a vertex from the query graph (see Figure 5); the second line indicates the name of an attribute of this vertex (the user can select which attributes to display: in this example only the "Name" attributes have been selected)

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-2

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p> protein-protein interactions where at least one of the two proteins has an annotated known function (Name !: "hypothetical"). (b) The GQL script describing the same query. GQL reserved keywords are indicated in bold. In the declaration of variable , the expression located to the right of the 'where' clause is a local constraint (here: the name must not contain ). In the declaration of , the expression located to the right of the 'where' clause is the global constraint (here: the two names must be different). (c) Result obtained by executing this query against the data graph shown in Figure 4b. When applied to the entire strain 26695 data set, this query yields 896 different answers

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-3

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p>ided with GenoLink. Classes are indicated by boxes (white arrows indicate inheritance) and association names are indicated in italics. For clarity, class and association attributes have not been indicated (an example is shown to the right part of the figure, with the Polypeptide class). The complete diagram is distributed with the GenoLink software documentation. (b) An example of data graph based on this data model. It represents a portion of the genome of the bacterium strain 26695 (NCBI RefSeq entry no. NC000915); IRO, ILO, ICF, IIG, HPA, CD and HPIW stand for edges that are instances of associations: IsRepliconOf, IsLocatedOn, IsCodingFor, IsInGeneOrtholog, HasPolypeptideAnnotation, ContainsDomain and HasPhysicalInteractionWith. The entire data graph for this genome actually contains 3197 vertices (1 Organism, 1 Replicon, 1576 ProteinGenes, 43 RNAGenes, 1576 Polypeptides) and 4664 edges (1 IsRepliconOf, 1619 IsLocatedOn, 1576 IsCodingFor and 1468 HasPhysicalInteractionWith). The dashed box displays the attributes for the Polypeptide ureB. COG, EC and IPR data are from the COG database [21], the Enzyme Commission database [24], and the InterPro database [23], respectively. Protein-protein interactions are public data available from Hybrigenics [30] and distributed with GenoLink

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-6

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p> it. This snapshot shows an example of result sub-graph corresponding to the Query Q7 (Table 1 [see ] and Figure 5). The edge linking the two Polypeptides corresponds to a physical interaction (HPIW). The red crosshair on the top-right of some vertices denotes that they are linked to some others that are not currently shown. These vertices may therefore be further expanded to gain more information about the full data graph. In this example, this operation has been performed on vertices holA and holB (from ) in order to display the corresponding Polypeptides (DNA polymerase III) that were not part of the query (see Figure 5)

Ollomo_PLoSPathog_2009_PHYML

Maximum likelihood tree inferred from the 4-gene concatenation using PHYML

Ollomo_PLoSPathog_2009

Nucleotide alignment concatenation of 4 mitochondrial genes for 17 Plasmodium species and one outgroup

Historic overview of the molecular descriptions and of the names given to the different lineages (seven lineages) of the <i>Laverania</i> subgenus.

<p>The lineage number (1 to 7) is given following the phylogeny presented in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat-1001283-g001" target="_blank">Figure 1A</a>.</p

Phylogeny of the <i>Laverania</i> subgenus.

<p>This phylogeny is based on partial <i>CytochromeB</i> sequences and including strains isolated and characterized in (A) Ollomo et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Ollomo1" target="_blank">[19]</a>, Prugnolle et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Prugnolle1" target="_blank">[22]</a>, Krief et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Krief1" target="_blank">[23]</a>, and Liu et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Liu1" target="_blank">[25]</a>, and in (B) Ollomo et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Ollomo1" target="_blank">[19]</a>, Prugnolle et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Prugnolle1" target="_blank">[22]</a>, Krief et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Krief1" target="_blank">[23]</a>, Duval et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Duval1" target="_blank">[24]</a>, and Liu et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Liu1" target="_blank">[25]</a>. The phylogenies were produced using a maximum likelihood approach and robustness was tested using 100 bootstraps. Names of the lineages were given following their first denomination (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat-1001283-t001" target="_blank">Table 1</a>) except for <i>P. billcollinsi</i>, which was first named by Rich et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001283#ppat.1001283-Rich2" target="_blank">[21]</a> as <i>P. reichenowi</i>.</p

Distribution of the different subspecies of chimpanzees, bonobos, and gorillas in Africa and representation of the spread of the different <i>Plasmodium</i> species in these subspecies.

<p>Distribution of the different subspecies of chimpanzees, bonobos, and gorillas in Africa and representation of the spread of the different <i>Plasmodium</i> species in these subspecies.</p

Location of the mosquito collection sites in Gabon.

<p>Location of the mosquito collection sites in Gabon.</p